setup .nf-core.yml lint

nf_core/lint/nfcore_yml.py

@@ -0,0 +1,61 @@
+def nfcore_yml(self):
+    """Repository ``.nf-core.yml`` tests
+
+    The ``.nf-core.yml`` contains metadata for nf-core tools to correctly apply its features.
+
+    * repository type:
+
+        * Check that the repository type is set.
+
+    * nf core version:
+
+         * Check if the nf-core version is set to the latest version.
+
+    """
+    passed = []
+    warned = []
+    failed = []
+
+    # Remove field that should be ignored according to the linting config
+    # ignore_configs = self.lint_config.get(".nf-core", [])
+
+    # with open(os.path.join(self.wf_path, ".nf-core.yml")) as fh:
+    #     content = fh.read()
+
+    # if "nextflow_badge" not in ignore_configs:
+    #     # Check that there is a readme badge showing the minimum required version of Nextflow
+    #     # [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
+    #     # and that it has the correct version
+    #     nf_badge_re = r"\[!\[Nextflow\]\(https://img\.shields\.io/badge/nextflow%20DSL2-!?(?:%E2%89%A5|%3E%3D)([\d\.]+)-23aa62\.svg\)\]\(https://www\.nextflow\.io/\)"
+    #     match = re.search(nf_badge_re, content)
+    #     if match:
+    #         nf_badge_version = match.group(1).strip("'\"")
+    #         try:
+    #             if nf_badge_version != self.minNextflowVersion:
+    #                 raise AssertionError()
+    #         except (AssertionError, KeyError):
+    #             failed.append(
+    #                 f"README Nextflow minimum version badge does not match config. Badge: `{nf_badge_version}`, "
+    #                 f"Config: `{self.minNextflowVersion}`"
+    #             )
+    #         else:
+    #             passed.append(
+    #                 f"README Nextflow minimum version badge matched config. Badge: `{nf_badge_version}`, "
+    #                 f"Config: `{self.minNextflowVersion}`"
+    #             )
+    #     else:
+    #         warned.append("README did not have a Nextflow minimum version badge.")
+
+    # if "zenodo_doi" not in ignore_configs:
+    #     # Check that zenodo.XXXXXXX has been replaced with the zendo.DOI
+    #     zenodo_re = r"/zenodo\.X+"
+    #     match = re.search(zenodo_re, content)
+    #     if match:
+    #         warned.append(
+    #             "README contains the placeholder `zenodo.XXXXXXX`. "
+    #             "This should be replaced with the zenodo doi (after the first release)."
+    #         )
+    #     else:
+    #         passed.append("README Zenodo placeholder was replaced with DOI.")
+
+    return {"passed": passed, "warned": warned, "failed": failed}